QC On Raw Data
Stephen Pederson
09 November, 2020
Last updated: 2020-11-09
Checks: 7 0
Knit directory: T47D_ZR75_DHT_StrippedSerum_RNASeq/analysis/
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library(ngsReports)
library(tidyverse)
library(yaml)
library(scales)
library(pander)
library(glue)
library(plotly)panderOptions("table.split.table", Inf)
panderOptions("big.mark", ",")
theme_set(theme_bw())config <- here::here("config/config.yml") %>%
read_yaml()
suffix <- paste0(config$tags$tag, config$ext)
sp <- config$ref$species %>%
str_replace("(^[a-z])[a-z]*_([a-z]+)", "\\1\\2") %>%
str_to_title()samples <- config$samples %>%
here::here() %>%
read_tsv() %>%
mutate(
R1 = paste0(sample, config$tags$r1, suffix),
R2 = paste0(sample, config$tags$r2, suffix),
) %>%
pivot_longer(
cols = c("R1", "R2"),
names_to = "Reads",
values_to = "Filename"
)config$analysis <- config$analysis %>%
lapply(intersect, y = colnames(samples)) %>%
.[vapply(., length, integer(1)) > 0]if (length(config$analysis)) {
samples <- samples %>%
unite(
col = group,
any_of(as.character(unlist(config$analysis))),
sep = "_", remove = FALSE
)
} else {
samples$group <- samples$Filename
}group_cols <- hcl.colors(
n = length(unique(samples$group)),
palette = "Zissou 1"
) %>%
setNames(unique(samples$group))fh <- round(6 + nrow(samples) / 15, 0)Quality Assessment on Raw Data
Hiseq_1
rawFqc <- here::here("data/raw/FastQC/Hiseq_1") %>%
list.files(pattern = "fastqc.zip", full.names = TRUE, recursive = TRUE) %>%
FastqcDataList() %>%
.[fqName(.) %in% samples$Filename]plotSummary(rawFqc)
Overall summary of FastQC reports
Library Sizes
A total of 32 libraries were contained in this dataset, with read totals ranging between 5,699,001 and 22,618,628 reads.
Across all libraries, reads were 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101 bases.
plotReadTotals(rawFqc, pattern = suffix, usePlotly = TRUE)Library Sizes for all supplied fastq files. Any samples run as multiple libraries are shown as the supplied multiple libraries and have not been merged.
Sequence Quality
plotBaseQuals(
rawFqc,
pattern = suffix,
usePlotly = TRUE,
dendrogram = TRUE,
cluster = TRUE
)Mean sequencing quality scores at each base position for each library
GC Content
plotGcContent(
x = rawFqc,
pattern = suffix,
species = sp,
gcType = "Trans",
usePlotly = TRUE,
dendrogram = TRUE,
cluster = TRUE
)GC content shown as the % above and below the theoretical GC content for the Hsapiens transcriptome.
ggplotly(
getModule(rawFqc, "Per_sequence_GC_content") %>%
group_by(Filename) %>%
mutate(
cumulative = cumsum(Count) / sum(Count)
) %>%
ungroup() %>%
left_join(samples) %>%
bind_rows(
getGC(gcTheoretical, sp, "Trans") %>%
mutate_at(sp, cumsum) %>%
rename_all(
str_replace_all,
pattern = sp, replacement = "cumulative",
) %>%
mutate(
Filename = "Theoretical GC",
group = Filename
)
) %>%
mutate(
group = as.factor(group),
group = relevel(group, ref = "Theoretical GC"),
cumulative = round(cumulative*100, 2)
) %>%
ggplot(aes(GC_Content, cumulative, group = Filename)) +
geom_line(aes(colour = group), size = 1/3) +
scale_x_continuous(label = ngsReports:::.addPercent) +
scale_y_continuous(label = ngsReports:::.addPercent) +
scale_colour_manual(
values = c("#000000", group_cols)
) +
labs(
x = "GC Content",
y = "Cumulative Total",
colour = "Group"
)
)GC content shown as a cumulative distribution for all libraries. Groups can be hidden by clicking on them in the legend.
Sequence Content
plotly::ggplotly(
getModule(rawFqc, module = "Per_base_sequence_content") %>%
mutate(Base = fct_inorder(Base)) %>%
group_by(Base) %>%
mutate(
across(c("A", "C", "G", "T"), function(x){x - mean(x)})
) %>%
pivot_longer(
cols = c("A", "C", "G", "T"),
names_to = "Nuc",
values_to = "resid"
) %>%
left_join(samples) %>%
ggplot(
aes(Base, resid, group = Filename, colour = group)
) +
geom_line() +
facet_wrap(~Nuc) +
scale_colour_manual(values = group_cols) +
labs(
x = "Read Position", y = "Residual", colour = "Group"
)
)Base and Position specific residuals for each sample. The mean base content at each position was calculated for each nucleotide, and the sample-specific residuals calculated.
AdapterContent
plotAdapterContent(
x = rawFqc,
pattern = suffix,
usePlotly = TRUE,
dendrogram = TRUE,
cluster = TRUE
)Total Adapter Content for each sample shown by starting position in the read.
Overrepresented Sequences
os <- suppressMessages(getModule(rawFqc, "Over"))
os_fh <- 6 + nrow(os) / 20if (nrow(os)){
if (length(unique(os$Filename)) > 1){
suppressMessages(
plotOverrep(
x = rawFqc,
pattern = suffix,
usePlotly = TRUE,
dendrogram = TRUE,
cluster = TRUE
)
)
}
}Summary of over-represented sequences across all libraries
os %>%
group_by(Sequence, Possible_Source) %>%
summarise(
`Found in` = n(),
Total = sum(Count),
`Largest Percent` = glue("{round(max(Percentage), 2)}%")
) %>%
pander(
caption = "*Summary of over-represented sequences within the raw data.*"
)| Sequence | Possible_Source | Found in | Total | Largest Percent |
|---|---|---|---|---|
| AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | No Hit | 1 | 19,652 | 0.34% |
| ACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAA | No Hit | 8 | 133,908 | 0.17% |
| ACTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG | No Hit | 3 | 32,989 | 0.15% |
| AGGGGAAGGCGCTTTGTGAAGTAGGCCTTATTTCTCTTGTCCTTTCGTAC | No Hit | 1 | 7,719 | 0.13% |
| AGGGGGAAGGCGCTTTGTGAAGTAGGCCTTATTTCTCTTGTCCTTTCGTA | No Hit | 1 | 12,229 | 0.21% |
| AGGGGTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT | No Hit | 1 | 14,213 | 0.25% |
| AGGTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTG | No Hit | 1 | 8,843 | 0.15% |
| ATAAGATTTGCCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGGGCA | No Hit | 2 | 22,020 | 0.15% |
| ATAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGAAGTAGGC | No Hit | 1 | 6,477 | 0.11% |
| ATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGAA | No Hit | 1 | 8,818 | 0.14% |
| ATAGAGGTGATGTTTTTGGTAAACAGGCGGGGTAAGATTTGCCGAGTTCC | No Hit | 1 | 6,168 | 0.1% |
| ATATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTG | No Hit | 2 | 32,228 | 0.24% |
| ATCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGGGATTTTTTAGGTA | No Hit | 1 | 8,194 | 0.13% |
| ATCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT | No Hit | 1 | 11,028 | 0.11% |
| ATGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT | No Hit | 2 | 14,480 | 0.12% |
| ATTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGC | No Hit | 1 | 7,451 | 0.12% |
| ATTGGTTATAATTTTTCATCTTTCCCTTGCGGTACTATATCTATTGCGCC | No Hit | 2 | 25,859 | 0.19% |
| CAAACCCACTCCACCCTACTACCAGACAACCTTAGCCAAACCATTTACCC | No Hit | 1 | 15,502 | 0.1% |
| CAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCC | No Hit | 6 | 99,368 | 0.14% |
| CAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTG | No Hit | 11 | 147,514 | 0.13% |
| CACCAGGTTGCCTAAGGAGGGGTGAACCGGCCCAGGTCGGAAACGGAGCA | No Hit | 13 | 249,151 | 0.19% |
| CACTATTTTGCTACATAGACGGGTGTGCTCTTTTAGCTGTTCTTAGGTAG | No Hit | 6 | 94,649 | 0.13% |
| CACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTAGAGGTGATGTTTT | No Hit | 8 | 147,927 | 0.19% |
| CAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAG | No Hit | 9 | 133,258 | 0.13% |
| CAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAG | No Hit | 12 | 280,879 | 0.21% |
| CATTCTCCTCCGCATAAGCCTGCGTCAGATTAAGACACTGAACTGACAAT | No Hit | 1 | 15,559 | 0.11% |
| CCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACC | No Hit | 5 | 67,457 | 0.11% |
| CCAACACAGGCATGCCCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTC | No Hit | 1 | 15,886 | 0.11% |
| CCAAGATAGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAA | No Hit | 9 | 143,664 | 0.19% |
| CCACTATTTTGCTACATAGACGGGTGTGCTCTTTTAGCTGTTCTTAGGTA | No Hit | 9 | 137,591 | 0.14% |
| CCAGCTATCACCAGGCTCGGTAGGTTTGTCGCCTCTACCTATAAATCTTC | No Hit | 1 | 12,710 | 0.1% |
| CCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCA | No Hit | 13 | 459,777 | 0.46% |
| CCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACC | No Hit | 1 | 6,661 | 0.12% |
| CCCAAACCCACTCCACCCTACTACCAGACAACCTTAGCCAAACCATTTAC | No Hit | 8 | 322,329 | 0.4% |
| CCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTAC | No Hit | 8 | 476,575 | 0.54% |
| CCCAAATAAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATA | No Hit | 2 | 37,273 | 0.12% |
| CCCAACACAGGCATGCCCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACT | No Hit | 7 | 113,224 | 0.14% |
| CCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGGACCTGTGGGTTT | No Hit | 2 | 32,648 | 0.12% |
| CCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAACTA | No Hit | 3 | 41,439 | 0.12% |
| CCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG | No Hit | 8 | 118,340 | 0.14% |
| CCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTT | No Hit | 16 | 318,686 | 0.21% |
| CCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTT | No Hit | 6 | 94,359 | 0.15% |
| CCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC | No Hit | 1 | 15,336 | 0.13% |
| CCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTA | No Hit | 3 | 45,229 | 0.14% |
| CCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGGACCTGTGGGTT | No Hit | 12 | 231,034 | 0.2% |
| CCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATAT | No Hit | 16 | 610,532 | 0.47% |
| CCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATA | No Hit | 6 | 91,213 | 0.16% |
| CCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATT | No Hit | 16 | 574,447 | 0.48% |
| CCCTGTTCTTGGGTGGGTGTGGGTATAATACTAAGTTGAGATGATATCAT | No Hit | 7 | 260,551 | 0.38% |
| CCCTGTTCTTGGGTGGGTGTGGGTATAATGCTAAGTTGAGATGATATCAT | No Hit | 7 | 280,267 | 0.47% |
| CCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGGGCATGCCTGTGTT | No Hit | 1 | 16,721 | 0.1% |
| CCGCACTAAGTTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGACCA | No Hit | 1 | 11,822 | 0.12% |
| CCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGTCC | No Hit | 3 | 50,876 | 0.13% |
| CCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTAC | No Hit | 1 | 6,976 | 0.12% |
| CCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCG | No Hit | 11 | 173,595 | 0.14% |
| CCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAG | No Hit | 5 | 87,355 | 0.15% |
| CCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAG | No Hit | 7 | 105,020 | 0.13% |
| CCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTG | No Hit | 16 | 395,723 | 0.31% |
| CCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTT | No Hit | 13 | 237,958 | 0.17% |
| CCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTA | No Hit | 8 | 146,451 | 0.19% |
| CCTGTTCTTGGGTGGGTGTGGGTATAATACTAAGTTGAGATGATATCATT | No Hit | 4 | 68,277 | 0.15% |
| CCTGTTCTTGGGTGGGTGTGGGTATAATGCTAAGTTGAGATGATATCATT | No Hit | 3 | 71,447 | 0.21% |
| CCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAA | No Hit | 1 | 6,831 | 0.12% |
| CCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG | No Hit | 16 | 1,215,558 | 0.87% |
| CCTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAA | No Hit | 1 | 7,128 | 0.13% |
| CCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCCTTGCGGTAC | No Hit | 12 | 262,326 | 0.23% |
| CGACCATCCCCGATAGAGGAGGACCGGTCTTCGGTCAAGGGTATACGAGT | No Hit | 1 | 7,089 | 0.12% |
| CGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGT | No Hit | 10 | 161,846 | 0.13% |
| CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCT | No Hit | 11 | 170,329 | 0.14% |
| CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCT | No Hit | 5 | 62,530 | 0.11% |
| CGCTGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAA | No Hit | 3 | 59,609 | 0.13% |
| CGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGT | No Hit | 14 | 240,765 | 0.18% |
| CGGGGGAAGGCGCTTTGTGAAGTAGGCCTTATTTCTCTTGTCCTTTCGTA | No Hit | 16 | 342,882 | 0.35% |
| CGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCA | No Hit | 2 | 24,946 | 0.12% |
| CGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACTTC | No Hit | 7 | 100,385 | 0.12% |
| CGTTAAACATGTGTCACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCT | No Hit | 6 | 99,704 | 0.15% |
| CGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTTCGCTTTGACTGG | No Hit | 14 | 303,781 | 0.22% |
| CTAACAGTTAAATTTACAAGGGGATTTAGAGGGTTCTGTGGGCAAATTTA | No Hit | 4 | 67,664 | 0.14% |
| CTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGAAGTAGGC | No Hit | 1 | 8,611 | 0.14% |
| CTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAG | No Hit | 16 | 296,583 | 0.21% |
| CTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGA | No Hit | 6 | 90,920 | 0.12% |
| CTAGAATAGGATTGCGCTGTTATCCCTAGGGTAACTTGTTCCGTTGGTCA | No Hit | 11 | 192,513 | 0.18% |
| CTAGAGGTGATGTTTTTGGTAAACAGGCGGGGTAAGATTTGCCGAGTTCC | No Hit | 4 | 61,385 | 0.16% |
| CTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA | No Hit | 1 | 12,887 | 0.11% |
| CTCAGACCGCGTTCTCTCCCTCTCACTCCCCAATACGGAGAGAAGAACGA | No Hit | 11 | 274,101 | 0.31% |
| CTCAGATCACGTAGGACTTTAATCGTTGAACAAACGAACCTTTAATAGCG | No Hit | 12 | 214,174 | 0.19% |
| CTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC | No Hit | 12 | 292,345 | 0.24% |
| CTCATTTGGATGTGTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTC | No Hit | 14 | 258,172 | 0.21% |
| CTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAG | No Hit | 8 | 178,021 | 0.21% |
| CTCCGAGGTCGCCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGG | No Hit | 16 | 330,108 | 0.25% |
| CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT | No Hit | 16 | 623,795 | 0.39% |
| CTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGA | No Hit | 16 | 621,595 | 0.55% |
| CTCGCTATGTTGCTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATC | No Hit | 7 | 108,012 | 0.13% |
| CTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGT | No Hit | 5 | 53,697 | 0.11% |
| CTCGGAGGTTGGGTTCTGCTCCGAGGTCGCCCCAACCGAAATTTTTAATG | No Hit | 10 | 181,804 | 0.17% |
| CTCGTATACCCTTGACCGAAGACCGGTCCTCCTCTATCGGGGATGGTCGT | No Hit | 1 | 16,776 | 0.1% |
| CTCGTCTGGTTTCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTT | No Hit | 9 | 160,533 | 0.2% |
| CTCTAAATCCCCTTGTAAATTTAACTGTTAGTCCAAAGAGGAACAGCTCT | No Hit | 13 | 252,600 | 0.23% |
| CTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGCTGTTCCTCTTTGGACTA | No Hit | 3 | 55,562 | 0.12% |
| CTCTAGAATAGGATTGCGCTGTTATCCCTAGGGTAACTTGTTCCGTTGGT | No Hit | 15 | 381,300 | 0.27% |
| CTCTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGCTGTTCCTCTTTGGAC | No Hit | 16 | 494,532 | 0.35% |
| CTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACT | No Hit | 16 | 385,293 | 0.27% |
| CTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACTTCAAATTC | No Hit | 10 | 152,647 | 0.14% |
| CTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGT | No Hit | 10 | 168,308 | 0.14% |
| CTGCTGTTTCCCGTGGGGGTGTGGCTAGGCTAAGCGTTTTGAGCTGCATT | No Hit | 8 | 160,451 | 0.23% |
| CTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCG | No Hit | 6 | 74,003 | 0.11% |
| CTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT | No Hit | 16 | 763,135 | 0.64% |
| CTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGA | No Hit | 5 | 65,325 | 0.11% |
| CTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTAGAGGTGATGTTTTTG | No Hit | 4 | 61,267 | 0.16% |
| CTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCAT | No Hit | 15 | 352,683 | 0.23% |
| CTGGTGATGCTAGAGGTGATGTTTTTGGTAAACAGGCGGGGTAAGATTTG | No Hit | 1 | 5,776 | 0.1% |
| CTGGTTTCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGT | No Hit | 14 | 316,880 | 0.29% |
| CTGTGGGCAAATTTAAAGTTGAACTAAGATTCTATCTTGGACAACCAGCT | No Hit | 3 | 31,305 | 0.12% |
| CTGTTCTTGGGTGGGTGTGGGTATAATACTAAGTTGAGATGATATCATTT | No Hit | 4 | 100,727 | 0.24% |
| CTGTTCTTGGGTGGGTGTGGGTATAATGCTAAGTTGAGATGATATCATTT | No Hit | 7 | 147,120 | 0.2% |
| CTTAATCTGACGCAGGCTTATGCGGAGGAGAATGTTTTCATGTTACTTAT | No Hit | 3 | 43,738 | 0.13% |
| CTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATGAC | No Hit | 6 | 94,100 | 0.13% |
| CTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAAC | No Hit | 9 | 169,128 | 0.18% |
| CTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCATTATGCA | No Hit | 4 | 62,197 | 0.19% |
| CTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGC | No Hit | 15 | 463,555 | 0.38% |
| CTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAA | No Hit | 2 | 39,372 | 0.14% |
| CTTATGAGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGT | No Hit | 4 | 75,653 | 0.16% |
| CTTATGGGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGT | No Hit | 2 | 30,622 | 0.12% |
| CTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAA | No Hit | 16 | 337,454 | 0.24% |
| CTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGAC | No Hit | 3 | 30,234 | 0.12% |
| CTTCTATAGGGTGATAGATTGGTCCAATTGGGTGTGAGGAGTTCAGTTAT | No Hit | 4 | 54,865 | 0.11% |
| CTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCT | No Hit | 1 | 15,174 | 0.12% |
| CTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCC | No Hit | 15 | 328,946 | 0.21% |
| CTTGGTTATAATTTTTCATCTTTCCCTTGCGGTACTATATCTATTGCGCC | No Hit | 14 | 423,849 | 0.51% |
| CTTTAATCGTTGAACAAACGAACCTTTAATAGCGGCTGCACCATCGGGAT | No Hit | 15 | 293,109 | 0.21% |
| CTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAAC | No Hit | 6 | 87,749 | 0.12% |
| CTTTCCTTATGAGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGA | No Hit | 6 | 110,254 | 0.18% |
| CTTTCCTTATGGGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGA | No Hit | 7 | 172,641 | 0.23% |
| CTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAACCGACCTGGATTACT | No Hit | 12 | 231,215 | 0.21% |
| GAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTC | No Hit | 7 | 95,555 | 0.13% |
| GATAGATTGGTCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGGGATT | No Hit | 4 | 78,926 | 0.2% |
| GCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT | No Hit | 1 | 14,949 | 0.1% |
| GCCTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGA | No Hit | 2 | 20,086 | 0.12% |
| GCTACCTTTGCACGGTTAGGGTACCGCGGCCGTTAAACATGTGTCACTGG | No Hit | 10 | 228,397 | 0.21% |
| GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG | No Hit | 1 | 16,405 | 0.11% |
| GCTGCTTTTAGGCCTACTATGGGTGTTAAATTTTTTACTCTCTCTACAAG | No Hit | 6 | 104,245 | 0.14% |
| GCTGTTAATTGTCAGTTCAGTGTCTTAATCTGACGCAGGCTTATGCGGAG | No Hit | 1 | 7,926 | 0.14% |
| GGCAAATTTAAAGTTGAACTAAGATTCTATCTTGGACAACCAGCTATCAC | No Hit | 5 | 90,918 | 0.16% |
| GGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACC | No Hit | 1 | 20,892 | 0.14% |
| GGCTGCACCATCGGGATGTCCTGATCCAACATCGAGGTCGTAAACCCTAT | No Hit | 1 | 13,281 | 0.11% |
| GGCTGCTTTTAGGCCTACTATGGGTGTTAAATTTTTTACTCTCTCTACAA | No Hit | 2 | 40,662 | 0.15% |
| GGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCA | No Hit | 3 | 71,259 | 0.19% |
| GGCTTATGCGGAGGAGAATGTTTTCATGTTACTTATACTAACATTAGTTC | No Hit | 1 | 21,986 | 0.1% |
| GGGAAGCTCATCAGTGGGGCCACGAGCTGAGTGCGTCCTGTCACTCCACT | No Hit | 1 | 16,984 | 0.12% |
| GGGATTTAGAGGGTTCTGTGGGCAAATTTAAAGTTGAACTAAGATTCTAT | No Hit | 1 | 21,473 | 0.1% |
| GGGGGAAGGCGCTTTGTGAAGTAGGCCTTATTTCTCTTGTCCTTTCGTAC | No Hit | 5 | 87,847 | 0.13% |
| GGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCAT | No Hit | 2 | 44,121 | 0.15% |
| GGGGTTAGTCCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCC | No Hit | 1 | 23,334 | 0.11% |
| GGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTG | No Hit | 6 | 180,914 | 0.32% |
| GGGTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTG | No Hit | 4 | 103,636 | 0.23% |
| GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA | No Hit | 10 | 158,914 | 0.13% |
| GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA | No Hit | 2 | 28,505 | 0.11% |
| GGTTAGTCCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCCTT | No Hit | 2 | 36,265 | 0.1% |
| GGTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTCTTAATCT | No Hit | 1 | 6,386 | 0.11% |
| GTAAGATTTGCCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGAGCA | No Hit | 5 | 112,114 | 0.2% |
| GTAAGATTTGCCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGGGCA | No Hit | 7 | 179,554 | 0.28% |
| GTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTG | No Hit | 8 | 208,260 | 0.26% |
| GTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTG | No Hit | 1 | 14,949 | 0.1% |
| GTCACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTAGAGGTGATGTT | No Hit | 3 | 51,730 | 0.11% |
| GTCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGGGATTTTTTAGGTA | No Hit | 10 | 205,131 | 0.28% |
| GTCCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCCTTGCGGT | No Hit | 1 | 11,330 | 0.1% |
| GTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAACCGACCTGGATT | No Hit | 7 | 150,702 | 0.17% |
| GTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACC | No Hit | 8 | 144,018 | 0.18% |
| GTCTGGTTTCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTA | No Hit | 1 | 6,480 | 0.11% |
| GTGAGGAGTTCAGTTATATGTTTGGGATTTTTTAGGTAGTGGGTGTTGAG | No Hit | 1 | 6,202 | 0.11% |
| GTGCTCTTTTAGCTGTTCTTAGGTAGCTCGTCTGGTTTCGGGGGTCTTAG | No Hit | 8 | 142,697 | 0.19% |
| GTGGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT | No Hit | 2 | 22,531 | 0.18% |
| GTGGGTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT | No Hit | 7 | 193,790 | 0.28% |
| GTGGGTGTTGAGCTTGAACGCTTTCTTAATTGGTGGCTGCTTTTAGGCCT | No Hit | 2 | 21,915 | 0.12% |
| GTTAAACATGTGTCACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTA | No Hit | 1 | 15,312 | 0.1% |
| GTTAAATTTTTTACTCTCTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGC | No Hit | 1 | 5,887 | 0.1% |
| GTTAATTGTCAGTTCAGTGTCTTAATCTGACGCAGGCTTATGCGGAGGAG | No Hit | 4 | 67,302 | 0.16% |
| GTTAATTGTCAGTTCAGTGTTTTAATCTGACGCAGGCTTATGCGGAGGAG | No Hit | 1 | 17,391 | 0.12% |
| GTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGG | No Hit | 15 | 308,472 | 0.2% |
| GTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTAGATATTGGGC | No Hit | 1 | 6,064 | 0.11% |
| GTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTCTTAATCTG | No Hit | 2 | 27,541 | 0.14% |
| GTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTTTTAATCTG | No Hit | 1 | 18,241 | 0.12% |
| TGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACT | No Hit | 1 | 18,589 | 0.12% |
| TGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAGACACTGAACT | No Hit | 8 | 123,241 | 0.15% |
| TGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCTAAGGAGGGGTGA | No Hit | 1 | 11,462 | 0.11% |
Hiseq_2
rawFqc <- here::here("data/raw/FastQC/Hiseq_2") %>%
list.files(pattern = "fastqc.zip", full.names = TRUE, recursive = TRUE) %>%
FastqcDataList() %>%
.[fqName(.) %in% samples$Filename]plotSummary(rawFqc)
Overall summary of FastQC reports
Library Sizes
A total of 32 libraries were contained in this dataset, with read totals ranging between 10,944,091 and 28,623,352 reads.
Across all libraries, reads were 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101 bases.
plotReadTotals(rawFqc, pattern = suffix, usePlotly = TRUE)Library Sizes for all supplied fastq files. Any samples run as multiple libraries are shown as the supplied multiple libraries and have not been merged.
Sequence Quality
plotBaseQuals(
rawFqc,
pattern = suffix,
usePlotly = TRUE,
dendrogram = TRUE,
cluster = TRUE
)Mean sequencing quality scores at each base position for each library
GC Content
plotGcContent(
x = rawFqc,
pattern = suffix,
species = sp,
gcType = "Trans",
usePlotly = TRUE,
dendrogram = TRUE,
cluster = TRUE
)GC content shown as the % above and below the theoretical GC content for the Hsapiens transcriptome.
ggplotly(
getModule(rawFqc, "Per_sequence_GC_content") %>%
group_by(Filename) %>%
mutate(
cumulative = cumsum(Count) / sum(Count)
) %>%
ungroup() %>%
left_join(samples) %>%
bind_rows(
getGC(gcTheoretical, sp, "Trans") %>%
mutate_at(sp, cumsum) %>%
rename_all(
str_replace_all,
pattern = sp, replacement = "cumulative",
) %>%
mutate(
Filename = "Theoretical GC",
group = Filename
)
) %>%
mutate(
group = as.factor(group),
group = relevel(group, ref = "Theoretical GC"),
cumulative = round(cumulative*100, 2)
) %>%
ggplot(aes(GC_Content, cumulative, group = Filename)) +
geom_line(aes(colour = group), size = 1/3) +
scale_x_continuous(label = ngsReports:::.addPercent) +
scale_y_continuous(label = ngsReports:::.addPercent) +
scale_colour_manual(
values = c("#000000", group_cols)
) +
labs(
x = "GC Content",
y = "Cumulative Total",
colour = "Group"
)
)GC content shown as a cumulative distribution for all libraries. Groups can be hidden by clicking on them in the legend.
Sequence Content
plotly::ggplotly(
getModule(rawFqc, module = "Per_base_sequence_content") %>%
mutate(Base = fct_inorder(Base)) %>%
group_by(Base) %>%
mutate(
across(c("A", "C", "G", "T"), function(x){x - mean(x)})
) %>%
pivot_longer(
cols = c("A", "C", "G", "T"),
names_to = "Nuc",
values_to = "resid"
) %>%
left_join(samples) %>%
ggplot(
aes(Base, resid, group = Filename, colour = group)
) +
geom_line() +
facet_wrap(~Nuc) +
scale_colour_manual(values = group_cols) +
labs(
x = "Read Position", y = "Residual", colour = "Group"
)
)Base and Position specific residuals for each sample. The mean base content at each position was calculated for each nucleotide, and the sample-specific residuals calculated.
AdapterContent
plotAdapterContent(
x = rawFqc,
pattern = suffix,
usePlotly = TRUE,
dendrogram = TRUE,
cluster = TRUE
)Total Adapter Content for each sample shown by starting position in the read.
Overrepresented Sequences
os <- suppressMessages(getModule(rawFqc, "Over"))
os_fh <- 6 + nrow(os) / 20if (nrow(os)){
if (length(unique(os$Filename)) > 1){
suppressMessages(
plotOverrep(
x = rawFqc,
pattern = suffix,
usePlotly = TRUE,
dendrogram = TRUE,
cluster = TRUE
)
)
}
}Summary of over-represented sequences across all libraries
os %>%
group_by(Sequence, Possible_Source) %>%
summarise(
`Found in` = n(),
Total = sum(Count),
`Largest Percent` = glue("{round(max(Percentage), 2)}%")
) %>%
pander(
caption = "*Summary of over-represented sequences within the raw data.*"
)| Sequence | Possible_Source | Found in | Total | Largest Percent |
|---|---|---|---|---|
| AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | No Hit | 1 | 93,244 | 0.42% |
| ACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAA | No Hit | 8 | 173,813 | 0.16% |
| ACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGAAGTAGG | No Hit | 1 | 17,151 | 0.1% |
| ATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGAA | No Hit | 1 | 30,784 | 0.18% |
| CAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCC | No Hit | 6 | 127,777 | 0.14% |
| CAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTG | No Hit | 14 | 260,671 | 0.14% |
| CACCAGGTTGCCTAAGGAGGGGTGAACCGGCCCAGGTCGGAAACGGAGCA | No Hit | 13 | 302,526 | 0.21% |
| CACTAAGTTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGACCACCA | No Hit | 2 | 27,331 | 0.11% |
| CACTATTTTGCTACATAGACGGGTGTGCTCTTTTAGCTGTTCTTAGGTAG | No Hit | 2 | 28,395 | 0.1% |
| CACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTAGAGGTGATGTTTT | No Hit | 8 | 169,158 | 0.15% |
| CAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAG | No Hit | 13 | 241,299 | 0.14% |
| CAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAG | No Hit | 13 | 418,818 | 0.27% |
| CATCAATATGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCTAAGG | No Hit | 1 | 15,507 | 0.11% |
| CATTCTCCTCCGCATAAGCCTGCGTCAGATTAAGACACTGAACTGACAAT | No Hit | 1 | 14,303 | 0.1% |
| CCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACC | No Hit | 4 | 71,126 | 0.11% |
| CCAACACAGGCATGCCCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTC | No Hit | 1 | 14,514 | 0.1% |
| CCAAGATAGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAA | No Hit | 7 | 158,572 | 0.2% |
| CCACTATTTTGCTACATAGACGGGTGTGCTCTTTTAGCTGTTCTTAGGTA | No Hit | 7 | 114,629 | 0.12% |
| CCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCA | No Hit | 13 | 582,257 | 0.53% |
| CCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACC | No Hit | 1 | 24,383 | 0.11% |
| CCCAAACCCACTCCACCCTACTACCAGACAACCTTAGCCAAACCATTTAC | No Hit | 8 | 407,385 | 0.39% |
| CCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTAC | No Hit | 8 | 606,167 | 0.56% |
| CCCAAATAAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATA | No Hit | 3 | 51,957 | 0.12% |
| CCCAACACAGGCATGCCCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACT | No Hit | 7 | 121,940 | 0.13% |
| CCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAACTA | No Hit | 1 | 11,845 | 0.11% |
| CCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG | No Hit | 9 | 169,932 | 0.14% |
| CCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTT | No Hit | 16 | 478,697 | 0.25% |
| CCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTT | No Hit | 8 | 191,307 | 0.18% |
| CCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC | No Hit | 1 | 12,552 | 0.1% |
| CCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTA | No Hit | 3 | 68,210 | 0.14% |
| CCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGGACCTGTGGGTT | No Hit | 13 | 252,438 | 0.16% |
| CCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATAT | No Hit | 16 | 894,791 | 0.53% |
| CCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATA | No Hit | 7 | 129,744 | 0.16% |
| CCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATT | No Hit | 16 | 807,766 | 0.5% |
| CCCTGTTCTTGGGTGGGTGTGGGTATAATACTAAGTTGAGATGATATCAT | No Hit | 8 | 380,667 | 0.4% |
| CCCTGTTCTTGGGTGGGTGTGGGTATAATGCTAAGTTGAGATGATATCAT | No Hit | 8 | 378,849 | 0.36% |
| CCGCACTAAGTTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGACCA | No Hit | 1 | 17,136 | 0.14% |
| CCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGTCC | No Hit | 5 | 91,285 | 0.13% |
| CCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTAC | No Hit | 1 | 27,978 | 0.12% |
| CCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCG | No Hit | 13 | 260,012 | 0.15% |
| CCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAG | No Hit | 7 | 137,481 | 0.13% |
| CCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAG | No Hit | 5 | 85,427 | 0.12% |
| CCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTG | No Hit | 16 | 593,917 | 0.3% |
| CCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTT | No Hit | 16 | 366,918 | 0.19% |
| CCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG | No Hit | 1 | 23,698 | 0.11% |
| CCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTA | No Hit | 7 | 154,193 | 0.16% |
| CCTGTTCTTGGGTGGGTGTGGGTATAATACTAAGTTGAGATGATATCATT | No Hit | 6 | 124,052 | 0.16% |
| CCTGTTCTTGGGTGGGTGTGGGTATAATGCTAAGTTGAGATGATATCATT | No Hit | 7 | 128,236 | 0.16% |
| CCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAA | No Hit | 1 | 26,038 | 0.12% |
| CCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG | No Hit | 16 | 1,559,454 | 0.88% |
| CCTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAA | No Hit | 1 | 25,086 | 0.11% |
| CCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCCTTGCGGTAC | No Hit | 9 | 221,481 | 0.2% |
| CGACCATCCCCGATAGAGGAGGACCGGTCTTCGGTCAAGGGTATACGAGT | No Hit | 1 | 18,094 | 0.11% |
| CGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGT | No Hit | 12 | 246,347 | 0.14% |
| CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCT | No Hit | 16 | 347,546 | 0.17% |
| CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCT | No Hit | 6 | 117,309 | 0.14% |
| CGCTATGTTGCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCC | No Hit | 2 | 27,049 | 0.1% |
| CGCTGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAA | No Hit | 4 | 74,579 | 0.12% |
| CGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGT | No Hit | 2 | 41,069 | 0.1% |
| CGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGT | No Hit | 15 | 349,005 | 0.21% |
| CGGGGGAAGGCGCTTTGTGAAGTAGGCCTTATTTCTCTTGTCCTTTCGTA | No Hit | 16 | 457,904 | 0.37% |
| CGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCA | No Hit | 1 | 21,393 | 0.13% |
| CGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACTTC | No Hit | 6 | 111,524 | 0.13% |
| CGTTAAACATGTGTCACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCT | No Hit | 6 | 113,034 | 0.14% |
| CGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTTCGCTTTGACTGG | No Hit | 16 | 436,986 | 0.22% |
| CTAACAGTTAAATTTACAAGGGGATTTAGAGGGTTCTGTGGGCAAATTTA | No Hit | 1 | 13,568 | 0.11% |
| CTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGAAGTAGGC | No Hit | 1 | 29,724 | 0.18% |
| CTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGC | No Hit | 2 | 28,325 | 0.1% |
| CTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAG | No Hit | 16 | 368,003 | 0.21% |
| CTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGA | No Hit | 4 | 63,221 | 0.11% |
| CTAGAATAGGATTGCGCTGTTATCCCTAGGGTAACTTGTTCCGTTGGTCA | No Hit | 7 | 128,374 | 0.14% |
| CTAGAGGTGATGTTTTTGGTAAACAGGCGGGGTAAGATTTGCCGAGTTCC | No Hit | 5 | 98,294 | 0.15% |
| CTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA | No Hit | 1 | 11,492 | 0.1% |
| CTCAGACCGCGTTCTCTCCCTCTCACTCCCCAATACGGAGAGAAGAACGA | No Hit | 12 | 315,306 | 0.3% |
| CTCAGATCACGTAGGACTTTAATCGTTGAACAAACGAACCTTTAATAGCG | No Hit | 10 | 183,605 | 0.17% |
| CTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC | No Hit | 13 | 427,555 | 0.27% |
| CTCATTTGGATGTGTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTC | No Hit | 15 | 352,489 | 0.24% |
| CTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAG | No Hit | 8 | 219,119 | 0.21% |
| CTCCGAGGTCGCCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGG | No Hit | 16 | 448,496 | 0.25% |
| CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT | No Hit | 16 | 1,043,647 | 0.53% |
| CTCCTCTATCGGGGATGGTCGTCCTCTTCGACCGAGCGCGCAGCTTCGGG | No Hit | 4 | 57,003 | 0.11% |
| CTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGA | No Hit | 16 | 929,900 | 0.63% |
| CTCGCTATGTTGCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATC | No Hit | 5 | 76,656 | 0.13% |
| CTCGCTATGTTGCTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATC | No Hit | 12 | 225,576 | 0.15% |
| CTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGT | No Hit | 1 | 24,681 | 0.11% |
| CTCGGAGGTTGGGTTCTGCTCCGAGGTCGCCCCAACCGAAATTTTTAATG | No Hit | 11 | 204,684 | 0.19% |
| CTCGTCTGGTTTCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTT | No Hit | 9 | 184,963 | 0.19% |
| CTCTAAATCCCCTTGTAAATTTAACTGTTAGTCCAAAGAGGAACAGCTCT | No Hit | 15 | 365,271 | 0.23% |
| CTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGCTGTTCCTCTTTGGACTA | No Hit | 1 | 12,457 | 0.1% |
| CTCTAGAATAGGATTGCGCTGTTATCCCTAGGGTAACTTGTTCCGTTGGT | No Hit | 16 | 447,090 | 0.25% |
| CTCTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGCTGTTCCTCTTTGGAC | No Hit | 16 | 553,925 | 0.3% |
| CTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACT | No Hit | 16 | 508,514 | 0.3% |
| CTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCT | No Hit | 1 | 12,628 | 0.11% |
| CTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACTTCAAATTC | No Hit | 10 | 200,257 | 0.15% |
| CTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGT | No Hit | 14 | 322,060 | 0.21% |
| CTGCTGTTTCCCGTGGGGGTGTGGCTAGGCTAAGCGTTTTGAGCTGCATT | No Hit | 13 | 319,794 | 0.24% |
| CTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCG | No Hit | 12 | 202,974 | 0.12% |
| CTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT | No Hit | 16 | 1,106,317 | 0.63% |
| CTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACG | No Hit | 1 | 13,698 | 0.11% |
| CTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGA | No Hit | 11 | 211,638 | 0.14% |
| CTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTAGAGGTGATGTTTTTG | No Hit | 4 | 75,891 | 0.12% |
| CTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCAT | No Hit | 15 | 477,543 | 0.26% |
| CTGGTGATGCTAGAGGTGATGTTTTTGGTAAACAGGCGGGGTAAGATTTG | No Hit | 1 | 25,606 | 0.11% |
| CTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAACTTAGT | No Hit | 1 | 12,518 | 0.1% |
| CTGGTTTCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGT | No Hit | 16 | 460,212 | 0.29% |
| CTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGG | No Hit | 1 | 20,247 | 0.1% |
| CTGTGGGCAAATTTAAAGTTGAACTAAGATTCTATCTTGGACAACCAGCT | No Hit | 2 | 42,223 | 0.11% |
| CTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTAG | No Hit | 1 | 17,726 | 0.1% |
| CTGTTCTTGGGTGGGTGTGGGTATAATACTAAGTTGAGATGATATCATTT | No Hit | 7 | 177,657 | 0.27% |
| CTGTTCTTGGGTGGGTGTGGGTATAATGCTAAGTTGAGATGATATCATTT | No Hit | 8 | 261,048 | 0.23% |
| CTTAATCTGACGCAGGCTTATGCGGAGGAGAATGTTTTCATGTTACTTAT | No Hit | 2 | 26,244 | 0.12% |
| CTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATGAC | No Hit | 8 | 140,910 | 0.14% |
| CTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAAC | No Hit | 8 | 189,049 | 0.18% |
| CTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCATTATGCA | No Hit | 5 | 107,292 | 0.2% |
| CTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGC | No Hit | 15 | 709,970 | 0.47% |
| CTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAA | No Hit | 4 | 72,194 | 0.13% |
| CTTATGAGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGT | No Hit | 7 | 135,664 | 0.15% |
| CTTATGGGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGACTTGT | No Hit | 4 | 63,705 | 0.12% |
| CTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAA | No Hit | 16 | 587,783 | 0.35% |
| CTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGAC | No Hit | 1 | 28,315 | 0.13% |
| CTTCTATAGGGTGATAGATTGGTCCAATTGGGTGTGAGGAGTTCAGTTAT | No Hit | 3 | 41,379 | 0.12% |
| CTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCT | No Hit | 4 | 71,784 | 0.13% |
| CTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCC | No Hit | 15 | 439,915 | 0.23% |
| CTTGGTTATAATTTTTCATCTTTCCCTTGCGGTACTATATCTATTGCGCC | No Hit | 16 | 651,782 | 0.5% |
| CTTTAATCGTTGAACAAACGAACCTTTAATAGCGGCTGCACCATCGGGAT | No Hit | 16 | 398,140 | 0.21% |
| CTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAAC | No Hit | 6 | 107,720 | 0.12% |
| CTTTCCTTATGAGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGA | No Hit | 7 | 158,822 | 0.17% |
| CTTTCCTTATGGGCATGCCTGTGTTGGGTTGACAGTGAGGGTAATAATGA | No Hit | 8 | 247,743 | 0.25% |
| CTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAACCGACCTGGATTACT | No Hit | 14 | 312,084 | 0.22% |
| CTTTGCACGGTTAGGGTACCGCGGCCGTTAAACATGTGTCACTGGGCAGG | No Hit | 2 | 25,395 | 0.11% |
| GAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTC | No Hit | 6 | 111,062 | 0.12% |
| GATAGATTGGTCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGGGATT | No Hit | 10 | 207,758 | 0.21% |
| GCACGGTTAGGGTACCGCGGCCGTTAAACATGTGTCACTGGGCAGGCGGT | No Hit | 1 | 12,994 | 0.11% |
| GCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT | No Hit | 1 | 16,483 | 0.11% |
| GCCTTATTTCTCTTGTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGA | No Hit | 2 | 47,035 | 0.16% |
| GCTACCTTTGCACGGTTAGGGTACCGCGGCCGTTAAACATGTGTCACTGG | No Hit | 13 | 335,892 | 0.21% |
| GCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCT | No Hit | 1 | 17,739 | 0.12% |
| GCTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT | No Hit | 1 | 17,185 | 0.12% |
| GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG | No Hit | 4 | 60,763 | 0.15% |
| GCTGCTTTTAGGCCTACTATGGGTGTTAAATTTTTTACTCTCTCTACAAG | No Hit | 6 | 109,346 | 0.14% |
| GCTGTTAATTGTCAGTTCAGTGTCTTAATCTGACGCAGGCTTATGCGGAG | No Hit | 1 | 32,093 | 0.14% |
| GGATTTTTTAGGTAGTGGGTGTTGAGCTTGAACGCTTTCTTAATTGGTGG | No Hit | 1 | 23,649 | 0.12% |
| GGCAAATTTAAAGTTGAACTAAGATTCTATCTTGGACAACCAGCTATCAC | No Hit | 7 | 159,774 | 0.17% |
| GGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACC | No Hit | 1 | 21,198 | 0.15% |
| GGCTGCACCATCGGGATGTCCTGATCCAACATCGAGGTCGTAAACCCTAT | No Hit | 1 | 12,431 | 0.11% |
| GGCTGCTTTTAGGCCTACTATGGGTGTTAAATTTTTTACTCTCTCTACAA | No Hit | 1 | 12,914 | 0.12% |
| GGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCA | No Hit | 3 | 67,584 | 0.19% |
| GGGAAGCTCATCAGTGGGGCCACGAGCTGAGTGCGTCCTGTCACTCCACT | No Hit | 1 | 17,749 | 0.12% |
| GGGATTTAGAGGGTTCTGTGGGCAAATTTAAAGTTGAACTAAGATTCTAT | No Hit | 2 | 35,530 | 0.1% |
| GGGATTTTTTAGGTAGTGGGTGTTGAGCTTGAACGCTTTCTTAATTGGTG | No Hit | 1 | 26,849 | 0.12% |
| GGGGATTTAGAGGGTTCTGTGGGCAAATTTAAAGTTGAACTAAGATTCTA | No Hit | 1 | 22,819 | 0.1% |
| GGGGGAAGGCGCTTTGTGAAGTAGGCCTTATTTCTCTTGTCCTTTCGTAC | No Hit | 4 | 75,442 | 0.13% |
| GGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCAT | No Hit | 3 | 62,401 | 0.14% |
| GGGGTTAGTCCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCC | No Hit | 1 | 20,509 | 0.1% |
| GGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTG | No Hit | 8 | 294,859 | 0.3% |
| GGGTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTG | No Hit | 6 | 158,012 | 0.21% |
| GGGTGATAGATTGGTCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGG | No Hit | 1 | 22,640 | 0.1% |
| GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA | No Hit | 13 | 288,399 | 0.18% |
| GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA | No Hit | 6 | 95,992 | 0.14% |
| GGTTAGTCCTTGCTATATTATGCTTGGTTATAATTTTTCATCTTTCCCTT | No Hit | 2 | 36,291 | 0.11% |
| GGTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTCTTAATCT | No Hit | 1 | 28,119 | 0.13% |
| GTAAGATTTGCCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGAGCA | No Hit | 8 | 215,866 | 0.22% |
| GTAAGATTTGCCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGGGCA | No Hit | 8 | 321,673 | 0.33% |
| GTAATAATGACTTGTTGGTTGATTGTAGATATTGGGCTGTTAATTGTCAG | No Hit | 2 | 32,467 | 0.12% |
| GTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTG | No Hit | 8 | 392,248 | 0.44% |
| GTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTG | No Hit | 2 | 32,126 | 0.12% |
| GTCAAGTTATTGGATCAATTGAGTATAGTAGTTCGCTTTGACTGGTGAAG | No Hit | 9 | 161,582 | 0.13% |
| GTCACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTAGAGGTGATGTT | No Hit | 5 | 85,663 | 0.12% |
| GTCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGGGATTTTTTAGGTA | No Hit | 15 | 414,966 | 0.29% |
| GTCCGCACTAAGTTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGAC | No Hit | 1 | 15,267 | 0.11% |
| GTCCTTTCGTACAGGGAGGAATTTGAAGTAGATAGAAACCGACCTGGATT | No Hit | 13 | 281,258 | 0.18% |
| GTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACC | No Hit | 15 | 312,082 | 0.2% |
| GTCTGGTTTCGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTA | No Hit | 5 | 92,344 | 0.13% |
| GTCTGTTCCAAGCTCCGGCAAAGGAGGCATCCGCCGGGCCCCTCCCCGAA | No Hit | 1 | 16,802 | 0.12% |
| GTGAGGAGTTCAGTTATATGTTTGGGATTTTTTAGGTAGTGGGTGTTGAG | No Hit | 1 | 27,307 | 0.12% |
| GTGATAGATTGGTCCAATTGGGTGTGAGGAGTTCAGTTATATGTTTGGGA | No Hit | 1 | 22,867 | 0.1% |
| GTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCATCAATATGGTG | No Hit | 2 | 28,998 | 0.12% |
| GTGCTCTTTTAGCTGTTCTTAGGTAGCTCGTCTGGTTTCGGGGGTCTTAG | No Hit | 13 | 317,419 | 0.21% |
| GTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGAT | No Hit | 4 | 66,105 | 0.12% |
| GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA | No Hit | 7 | 133,657 | 0.18% |
| GTGGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT | No Hit | 7 | 171,068 | 0.25% |
| GTGGGTATAATGCTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT | No Hit | 8 | 354,207 | 0.37% |
| GTGGGTGTTGAGCTTGAACGCTTTCTTAATTGGTGGCTGCTTTTAGGCCT | No Hit | 8 | 165,631 | 0.15% |
| GTTAAACATGTGTCACTGGGCAGGCGGTGCCTCTAATACTGGTGATGCTA | No Hit | 2 | 29,070 | 0.11% |
| GTTAAATTTTTTACTCTCTCTACAAGGTTTTTTCCTAGTGTCCAAAGAGC | No Hit | 3 | 61,549 | 0.14% |
| GTTAATTGTCAGTTCAGTGTCTTAATCTGACGCAGGCTTATGCGGAGGAG | No Hit | 7 | 172,454 | 0.23% |
| GTTAATTGTCAGTTCAGTGTTTTAATCTGACGCAGGCTTATGCGGAGGAG | No Hit | 1 | 18,826 | 0.14% |
| GTTCCTTTTACTTTTTTTAACCTTTCCTTATGGGCATGCCTGTGTTGGGT | No Hit | 1 | 23,023 | 0.1% |
| GTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGG | No Hit | 15 | 417,024 | 0.23% |
| GTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTAGATATTGGGC | No Hit | 3 | 57,903 | 0.14% |
| GTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTCTTAATCTG | No Hit | 7 | 167,214 | 0.17% |
| GTTGATTGTAGATATTGGGCTGTTAATTGTCAGTTCAGTGTTTTAATCTG | No Hit | 2 | 39,283 | 0.15% |
| GTTGGGTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTAGATAT | No Hit | 2 | 41,367 | 0.11% |
| GTTTTTGGTAAACAGGCGGGGTAAGATTTGCCGAGTTCCTTTTACTTTTT | No Hit | 2 | 35,451 | 0.12% |
| NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | No Hit | 10 | 460,429 | 0.43% |
| TATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTGTGA | No Hit | 3 | 56,996 | 0.13% |
| TCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCA | No Hit | 1 | 14,689 | 0.12% |
| TCCAGGTCGGTTTCTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAA | No Hit | 1 | 13,043 | 0.11% |
| TGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACT | No Hit | 1 | 16,358 | 0.12% |
| TGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAGACACTGAACT | No Hit | 8 | 159,789 | 0.15% |
| TGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGAC | No Hit | 1 | 12,122 | 0.1% |
| TGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCTAAGGAGGGGTGA | No Hit | 1 | 16,601 | 0.14% |
| TGTGGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCT | No Hit | 1 | 25,034 | 0.11% |
| TTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTT | No Hit | 1 | 22,823 | 0.1% |
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] plotly_4.9.2.1 glue_1.4.2 pander_0.6.3
[4] scales_1.1.1 yaml_2.2.1 forcats_0.5.0
[7] stringr_1.4.0 dplyr_1.0.2 purrr_0.3.4
[10] readr_1.4.0 tidyr_1.1.2 tidyverse_1.3.0
[13] ngsReports_1.6.0 tibble_3.0.4 ggplot2_3.3.2
[16] BiocGenerics_0.36.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 hwriter_1.3.2
[3] ellipsis_0.3.1 rprojroot_1.3-2
[5] XVector_0.30.0 GenomicRanges_1.42.0
[7] ggdendro_0.1.22 fs_1.5.0
[9] rstudioapi_0.11 farver_2.0.3
[11] ggrepel_0.8.2 DT_0.16
[13] fansi_0.4.1 lubridate_1.7.9
[15] xml2_1.3.2 leaps_3.1
[17] knitr_1.30 jsonlite_1.7.1
[19] Rsamtools_2.6.0 Cairo_1.5-12.2
[21] broom_0.7.2 cluster_2.1.0
[23] dbplyr_2.0.0 png_0.1-7
[25] compiler_4.0.3 httr_1.4.2
[27] backports_1.2.0 assertthat_0.2.1
[29] Matrix_1.2-18 lazyeval_0.2.2
[31] cli_2.1.0 later_1.1.0.1
[33] htmltools_0.5.0 tools_4.0.3
[35] gtable_0.3.0 GenomeInfoDbData_1.2.4
[37] reshape2_1.4.4 FactoMineR_2.3
[39] ShortRead_1.48.0 Rcpp_1.0.5
[41] Biobase_2.50.0 cellranger_1.1.0
[43] vctrs_0.3.4 Biostrings_2.58.0
[45] crosstalk_1.1.0.1 xfun_0.19
[47] rvest_0.3.6 lifecycle_0.2.0
[49] zlibbioc_1.36.0 MASS_7.3-53
[51] zoo_1.8-8 hms_0.5.3
[53] promises_1.1.1 MatrixGenerics_1.2.0
[55] SummarizedExperiment_1.20.0 RColorBrewer_1.1-2
[57] latticeExtra_0.6-29 stringi_1.5.3
[59] highr_0.8 S4Vectors_0.28.0
[61] BiocParallel_1.24.0 GenomeInfoDb_1.26.0
[63] rlang_0.4.8 pkgconfig_2.0.3
[65] matrixStats_0.57.0 bitops_1.0-6
[67] evaluate_0.14 lattice_0.20-41
[69] labeling_0.4.2 GenomicAlignments_1.26.0
[71] htmlwidgets_1.5.2 tidyselect_1.1.0
[73] here_0.1 plyr_1.8.6
[75] magrittr_1.5 R6_2.5.0
[77] IRanges_2.24.0 generics_0.1.0
[79] DelayedArray_0.16.0 DBI_1.1.0
[81] pillar_1.4.6 haven_2.3.1
[83] whisker_0.4 withr_2.3.0
[85] scatterplot3d_0.3-41 RCurl_1.98-1.2
[87] modelr_0.1.8 crayon_1.3.4
[89] rmarkdown_2.5 jpeg_0.1-8.1
[91] grid_4.0.3 readxl_1.3.1
[93] data.table_1.13.2 git2r_0.27.1
[95] reprex_0.3.0 digest_0.6.27
[97] flashClust_1.01-2 httpuv_1.5.4
[99] stats4_4.0.3 munsell_0.5.0
[101] viridisLite_0.3.0